He has authored over 350 scientific papers and is the recipient of several international honors and awards, including the Ramon y Cajal Award in Neuroscience (Spain), the Norman Geschwind Prize in Behavioral Neurology from the American Academy of Neurology, the Friedrich Wilhelm Bessel Research Award from The Alexander von Humboldt Foundation (Germany), and the Jean Signoret Prize from the Ipsen Foundation (France). In 2000, he won the Daniel D. Federman Outstanding Clinical Educator Award. He is a member of the Spanish Royal Academy of Pharmacy.

Pascual-Leone is a world leader in the development of transcranial magnetic stimulation for application in cognitive neuroscience and for therapeutic applications in neurology, psychiatry and neurorehabilitation. Pascual-Leone's research projects aim at understanding the mechanisms that control brain plasticity across the lifespan to be able to modify them for the subject’s optimal behavioral outcome. Pascual-Leone combines various brain imaging and brain stimulation methodologies to establish a causal relationship and a precise chronometry between regional brain activation and behavior, and uses noninvasive brain stimulation techniques to modulate brain plasticity, suppressing some changes and enhancing others, to gain a clinical benefit and behavioral advantage for a given individual. Such non-invasive approaches can lead to clinically relevant therapeutic effects in neuropsychiatry and neurorehabilitation, and serve as proof-of-principle prior to more invasive neuromodulatory interventions.